Extend The Coordinates Entries Within A Bed File

Question

[alon.goren]

Hi,

I want to extend the coordinates entries within a bed file.

I tried using BedextendRanges, but it extends only on one end, and requires strand information.

Using awk is problematic, as it doesn't take into account the genome size...

Is there a tool for such?

Thanks!

Alon.

Answer 1

[Istvan Albert]

You can use the slop utility in bedtools or the range option in the bedops suite:

 $ bedtools slop

Tool:    bedtools slop (aka slopBed)
Version: v2.16.2
Summary: Add requested base pairs of "slop" to each feature.

Usage:   bedtools slop [OPTIONS] -i <bed/gff/vcf> -g <genome> [-b <int> or (-l and -r)]

Options: 
    -bIncrease the BED/GFF/VCF entry -b base pairs in each direction.
        - (Integer) or (Float, e.g. 0.1) if used with -pct.

...

Answer 2

[Alex Reynolds]

The bedops tool in the BEDOPS suite does this, as well, with the use of the --range operator, specifying L and R as left and right shifts. You can specify negative values in either direction to "shrink" or shift elements (the latter useful for indexing changes). Zero-length elements, where found, are left out of results, and left padding will extend elements to the zero-th position:

bedops --range L:R --everything foo.bed > adjustedFoo.bed

One more option, perhaps. BEDOPS is deliberately agnostic about genomes, so this won't limit coordinates on the right bound, but that's easily addressed with awk and end boundary values specific to your genome and chromosomes.